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Data for: Long-wavelength-sensitive (lws) opsin gene expression, foraging and visual communication in coral reef fishes

Citation

Stieb, Sara et al. (2022), Data for: Long-wavelength-sensitive (lws) opsin gene expression, foraging and visual communication in coral reef fishes, Dryad, Dataset, https://doi.org/10.5061/dryad.qv9s4mwgf

Abstract

Coral reef fishes are diverse in ecology and behaviour and show remarkable colour variability.  Investigating the visual pigment gene (opsin) expression in these fishes makes it possible to associate their visual genotype and phenotype (spectral sensitivities) to visual tasks such as feeding strategy or conspecific detection. By studying relative opsin expression in all major damselfish clades (Pomacentridae) and representatives from five other coral reef fish families, we show that the long-wavelength-sensitive (lws) opsin gene is highly expressed in algivorous and less or not expressed in zooplanktivorous species. Lws is also upregulated in species with orange/red colours (reflectance starting beyond 520nm) and expression is highest in orange/red-coloured algivores. Visual models from the perspective of a typical damselfish indicate that sensitivity to longer wavelengths (indicated by the expression of LWS) does enhance the ability to detect the red to far-red component of algae and orange/red-coloured conspecifics, possibly enabling social signalling.

Character state reconstructions indicate that in the early evolutionary history of damselfishes, no sensitivity to long wavelength (no lws expression) and no orange/red colouration and almost equal probabilities for being an algivore, omnivore or zooplanktivores, were present. Sensitivity to long wavelength (increased lws expression) only emerged in association with a specialization to algivory but never to zooplanktivory. Furthermore, higher lws expression is also exploited by social signalling in orange/red, which emerged after the transition to algal feeding. Although variability in reconstructions of the relative timing of these traits may deviate and alternative explanations are possible, our results are consistent with sensory bias explaining diversification of social signals. 

Methods

Guide to supplementary data and files

1. The damselfish phylogeny alignment contains species used in this study being modified from The Fish Tree of Life (Rabosky et al., 2018) and is used for ancestral state reconstructions

2. Data used for visual models as reflectance data of backgrounds, algae, fish colours, ambient illuminant measurements and the damselfish lens transmittance. 

3. R-code used for visual models 

4. The alignment to reconstruct maximum-likelihood amino acid trees of newly sequenced opsin genes

5. Coral reef fish reflectances measured in this study; data are presented as non-normalized data and averaged per species for multiple measurements across several and within one specimen

6. R-code used for ancestral state reconstructions (corHMM)

7. The alignment to reconstruct maximum-likelihood trees of damselfish species used for ancestral state reconstructions

Usage Notes

Guide to supplementary data and files

1. The damselfish phylogeny on which ancestral states are reconstructed: damselfish phylogeny alignment .fasta

2. Data used for visual models: data for visual models.cvs

3. The R-code used for visual models: visual model Rscript_I AquaVis4T_needed.R

4. The alignment for the tree of newly sequenced opsin genes: new opsins coral reef fish alignment.fasta

5. Coral reef fish reflectances maesured in this study: spectral reflectance fish colours .csv

6. The R-code used for ancestral state reconstructions (corHMM): corHMMdamselfish_LJdQ.R

7. The alignment for the damselfish phylogeny tree used for ancestral state reconstructions: aligment_corHMM.fasta